ReadSortOptionParser.java

// Copyright (C) 2011-2012 CRS4.
//
// This file is part of Seal.
//
// Seal is free software: you can redistribute it and/or modify it
// under the terms of the GNU General Public License as published by the Free
// Software Foundation, either version 3 of the License, or (at your option)
// any later version.
//
// Seal is distributed in the hope that it will be useful, but
// WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
// or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
// for more details.
//
// You should have received a copy of the GNU General Public License along
// with Seal.  If not, see <http://www.gnu.org/licenses/>.

package it.crs4.seal.read_sort;

import it.crs4.seal.common.SealToolParser;
import it.crs4.seal.common.ClusterUtils;

import java.util.ArrayList;
import java.io.IOException;

import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.Path;

import org.apache.commons.cli.*;

public class ReadSortOptionParser extends SealToolParser {

	public static final String ConfigSection = "ReadSort";

	private Option ann;
	private Option distReference;

	@SuppressWarnings("static") // for OptionBuilder
	public ReadSortOptionParser()
	{
		super(ConfigSection, "seal read_sort");

		// define the custom options
		ann = OptionBuilder
		        .withDescription("annotation file (.ann) of the BWA reference used to create the SAM data")
		        .hasArg()
		        .withArgName("ref.ann")
		        .withLongOpt("annotations")
		        .create("ann");
		options.addOption(ann);

		distReference = OptionBuilder
		        .withDescription("BWA reference on HDFS used to create the SAM data, to be distributed by DistributedCache")
			      .hasArg()
			      .withArgName("archive")
			      .withLongOpt("distributed-reference")
			      .create("distref");
		options.addOption(distReference);

		this.setMinReduceTasks(1);
	}

	@Override
	protected CommandLine parseOptions(Configuration conf, String[] args)
	  throws IOException, ParseException
	{
		CommandLine line = super.parseOptions(conf, args);

		/********* distributed reference and annotations *********/
		if (line.hasOption(distReference.getOpt()))
		{
			// Distribute the reference archive, and create a // symlink "reference" to the directory
			Path optPath = new Path(line.getOptionValue(distReference.getOpt()));
			optPath = optPath.makeQualified(optPath.getFileSystem(conf));
			Path cachePath = new Path(optPath.toString() + "#reference");
			conf.set("mapred.cache.archives", cachePath.toString());
			conf.set("mapred.create.symlink", "yes");

			if (line.hasOption(ann.getOpt()))
				conf.set(ReadSort.REF_ANN_PROP_NAME, "reference/" + line.getOptionValue(ann.getOpt()));
			else
				throw new ParseException("You must specify the name of the annotation file within the distributed reference archive with -" + ann.getOpt());
		}
		else if (line.hasOption(ann.getOpt()))
		{
			// direct access to the reference annotation
			conf.set(ReadSort.REF_ANN_PROP_NAME, line.getOptionValue(ann.getOpt()));
		}
		else
			throw new ParseException("You must provide the path the reference annotation file (<ref>.ann)");

		conf.set(ClusterUtils.NUM_RED_TASKS_PROPERTY, String.valueOf(getNReduceTasks()));
		return line;
	}
}